OK, The only way I can re-boot is to unplug Toppy then re-connect.
As I press home the plug I have the remote 0 button pressed, within a couple of feet of Toppy.
Toppy's text display goes from blank, to 'Loading' and then to 'Run'. All this time no 'Signal acknowledge' indicator shows.
There is a blank pause between 'Loading' and 'Run', also with Toppy disconnected the screen is just blue.
As 'Loading' goes off, the screen goes black then 'Run' shows and a second or so after that the picture starts to appear and comprises Toppy's native channel display and a very broken picture arrives a few moments later.
I leave the 0 button pressed all this time, and 'Run' continues to show and the picture starts moving... all still very broken, and the TV just stays like that until I give up, it's been 15 minutes a few times.

I have also, when the picture starts, release the 0 button and pressed the (original) Archive button... no change whatsoever.
I've tried the same thing but this time using the programmed Archive button (List), again nothing.
If I press the remote 'Off' (Standby) button nothing at all happens. Oh... once I've released the 0 button to try other options, the 'Signal acknowledge' indicator is active from then on.
If I press Toppy's front panel On / Off button 'Wait' appears in the display and just stays there, again over 15 minutes.

To run it, go to the native archive*, press << to get to /ProgramFiles, navigate to Utilities, use the up/down arrow to get to Channel Organiser and press OK.

* With no TAPs running, just press archive.

If MyStuff is running, it will depend on your settings.

If you have L8: Display Toppy Archive from MyStuff Archive=Yes (the default), then press Archive twice

If you have TimeShifting enabled on the main Toppy menu, press the Play button to bring up the playbar, and then press archive (with any native Toppy overlay on the screen, pressing a button will force that button's native action, bypassing any TAPs)

If neither of the above is true, press Info, then Menu, then select the last option on the MyStuff menu (if you start at A1, you can press Up to get to the bottom) to exit MyStuff

Did as Andy suggested and removed the HDD from the equation.
Booted up Toppy, and was able to access 'Factory Reset' (Did it)
Did a manual installation using just the Emley Moor channels.
Reconnected HDD, re-booted,.. So far, so good.
Tried running Channel Organiser... Failed.
Used the native Toppy way to remove the detritus.
Went back over Julie's instructions and experimented a bit and finally managed to get CO to work
Ok, I see what you mean Julie... Nice n easy...
CO did a reload of all the channels I'd deleted, but I noticed, just from Emley Moor, but I had opted for 'this TX'.
CO then proceeded to offer to remove all the unwanted ones... without having to re-select them. (Did that)
So... Toppy's back how it was plus I know how to access CO.
Next, I checked in folder Program Files/Settings/Logos and found two files:

datlogo.dat_______694 kb
datsmlogo.dat____ 694 kb

So... I (Just) did another re-boot, then waited for the (L) & (S) (Load & Search ?) to complete and tried EPG again...
Back where it all started... No logos !
I get the Channel Names with the little progress bar beneath, but no logo.

Looks like the "red" dat was the icon displayed by TopManager to indicate the type of file... Looks like the brown colour I chose to me...

Was there a logos.lnk file? : No, but there was on a previous occasion when there were no x.dat files.
Did you restart MyStuff (or reboot the toppy) after loading the files? : I'd just done a re-boot prior to making the post.
Did you use TM "Tools|Install Tap| MyStuff Logos" to install them? : At one time the x.dat weren't in the folder. Since then I've re-installed MyStuf at least once, maybe as many as three times now, using C:\MyStuff64Installer\SetUp.exe (Unzipped from web download).
Please post your MyStuff Settings :

Grid EPG/Grid Now & Next
C1: Display progress bars=Yes
C2: Cell style=Rounded
C3: Display MoreProgram indicators in Grid EPG=Yes
C4: Number of channels/font size=10/Small
C5: Number of hours to display in Grid EPG=3 Hrs
C6: Channel to show at top of Grid EPG/Grid Now & Next=Current (M)
C7: Time for left hand edge of Grid EPG=Now - 15m
C8: Style of Now Line in Grid EPG=Full (2)
C9: Transparency of Now Line in Grid EPG=Solid

EPG Chain
E1: View on first press of the EPG key=Grid EPG
E2: View on second press of the EPG key=Grid N&N
E3: View on third press of the EPG key=Toppy EPG
E4: View on fourth press of the EPG key=Off

Now & Next
F1: Display extra gap below Now & Next=No
F2: Display Now & Next on channel change=None
F3: Now & Next display duration (seconds)=Til Exit
F4: Now & Next auto display duration (seconds)=1
F5: Number of extra programs on Now & Next=0
F6: Number of extra programs on extended Now & Next=5
F7: Expand Now & Next to display full program information=Yes
F8: Display descriptions for extra programmes=No
F9: Display extra programmes in 2 columns=No

Now & Next Chain
G1: View on first press of the Now & Next key, and on Screensaver=Normal
G2: View on second press of the Now & Next key=Extended
G3: View on third press of the Now & Next key=Off
G4: View on fourth press of the Now & Next key=Off
G5: Activate Now & Next chain from arrow keys=No

Extended Info
H1: Large font on Extended Info=No
H2: Description to show in Extended Info=Normal

Searches
K1: Number of days to search for Text/PowerSearches=14
K2: Adjust manual timers for schedule changes=Yes
K3: Channels to search by default=All
K4: Search PlusOne channels by default=No
K5: AutoFile new Searches by default=No
K6: Show programme name folders in Move To=Yes
K7: Merge back to back timers=No
K8: Retain part watched recordings on Keep Searches=Yes
K9: Type of Search to create on pressing SlowMo=Menu
K10: Type of Search to create on pressing Blue=Power
K11: Offer to record Series on pressing Record=Always
K12: Search validity period=48 weeks